a) and b) are never correct, because "are fallen" and "was fallen" are grammatically incorrect. The tenses [verb to be] + [past participle of intransitive verb] is not a tense in Modern English. *
c) is correct, because the verb is in the present perfect tense, which tells us about an action occurred at some nonspecific point in time before the present moment.
d) is not correct, because the verb is in the past perfect tense, which tells us an action occurred at a nonspecific point in time before some other event in the past. Therefore it is not okay to use, because there is no other event you are comparing to. If your son asked you about the tree later that day,
Why didn't that tree have leaves?
You could respond
The tree was without leaves because the leaves had fallen on the ground.
Because you are comparing to a verb in the past tense. Basically the past perfect is a "super" past tense.
*As user chumakoff points out, phrases like "He is gone" is really common in modern English. And yet, "He is come" sounds strange to me. Both of these fit the pattern [verb to be] + [past participle of intransitive verb]. The only difference is one uses the verb "to go", the other the verb "to come". So why don't people say "He is come" to mean "He is here"?
I suspect that the construction [verb to be] + [past participle of intransitive verb] used to be valid syntax, but is no longer valid for the majority of verbs. "He is gone" is an idiom, and only sounds like current day English because of frequent daily use. In fact, "gone" in this context doesn't have the full powers of a verb. For example, although,
I go to Spain
is valid syntax, people don't usually say
He is gone to Spain
They would instead say
He has gone to Spain